Dear AMBER users:
It is widely used technique to mimic the the influence of solvent using
implicit solvent(Generally, water). In AMBER, my understanding is that
there are two methods to use implicit solvent. One is Generalized-Born
(GB) model , and the other is to use distance-dependent dielectric
model. Beause there is no GB model implemented in NMODE, so I use
distantce-dependent dielectic model when I perform normal mode analysis
of nucleic acids. My question is concering about the distance-dependent
model in AMBER.
Based on the Debye-H